A collection of useful sequencing utilities.
As I have done in the past, I intend to develop
seq-kit over a period of months or years. In general, this means I'll add a new tool or utility when it becomes apparent that I need it.
However, I am open to PRs, requests, and feedback. Please let me know what you think.
I intend to port some commands over from VCF-kit, but will broaden the applicability to FASTQs, BAMs, and perhaps even other items.
- fa-gc - Calculates GC content surrounding a given genomic position at specified window sizes.
- fq-dedup - The
fq-dedupcommand de-duplicates a FASTQ by read ID.
- fq-count - Count the number of reads in a FASTQ and other metrics.
- fq-meta - Provides basic information and a best guess as to sequencer from FASTQs.
- insert-size - Calculates insert-size quickly.
- json - Convert VCF output to JSON.
- sample - Samples variants from a VCF.
- iter - generates genomic ranges for parallelizing commands.
- rand - Generates random sites and regions from FASTA, BAM, and VCF